Thanks for the feedback! I've just done that!
Radu On Fri, Apr 27, 2018 at 8:40 PM, Hervé Pagès <hpa...@fredhutch.org> wrote: > On 04/27/2018 12:31 PM, Radu Zabet wrote: > >> Thank you for that Herve! >> >> I managed to figure out what the problem was. >> >> I was using a GRangesList constructor and, when validating the argument >> passed to the function, I was checking if the class was GRangesList instead >> of CompressedGRangesList. >> > > CompressedGRangesList is a subclass of virtual class GRangesList that > uses a particular internal representation to store the list in an > efficient manner. > > Note that it's alway better to use is(x, "GRangesList") for this kind > of checks. The exact class of 'x' does not matter as long as 'x' derives > from GRangesList. Doing class(x) == "CompressedGRangesList" will be > FALSE if 'x' is another GRangesList derivative and that is probably not > what you want. > > Cheers, > H. > > >> Radu >> >> On Fri, Apr 27, 2018 at 8:11 PM, Hervé Pagès <hpa...@fredhutch.org >> <mailto:hpa...@fredhutch.org>> wrote: >> >> Hi Radu, >> >> DMRcaller is all green on today's report: >> >> https://bioconductor.org/checkResults/3.7/bioc-LATEST/DMRcaller/ >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__ >> bioconductor.org_checkResults_3.7_bioc-2DLATEST_DMRcaller_&d=DwMFaQ&c= >> eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJ >> KaaPhzWA&m=sC2oO3c16mMorqdk5d8nvHzqg1dL7v228YdPl836xng&s=FzU >> y1jhF6u2fVJ4oNL_dP1E2-djzZldXsth0bOXXfEg&e=> >> >> Remember that after you update (and push to git.bioconductor.org >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__git. >> bioconductor.org&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3Xe >> AvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=sC2oO3c16mMorqdk5d8nv >> Hzqg1dL7v228YdPl836xng&s=XmaKhXkb20E2q6udR5bDulIMCnvWq3qxtVUhHLOTZiQ&e=>) >> you >> need to wait at least 18h before the update is visible on the build >> report. 18h is if you pushed right before the builds start (the >> software >> builds start every day at 4:45 pm EST). If you push right after the >> builds start then you will need to wait 42h! >> >> Cheers, >> H. >> >> On 04/20/2018 07:47 AM, Radu Zabet wrote: >> >> Hi everyone, >> >> I am the maintainer of DMRcaller. I did an update yesterday and >> on the >> build report today, the package failed with the error. >> >> Error: processing vignette 'DMRcaller.Rnw' failed with >> diagnostics: >> methylationProfile needs to be a GRangesList >> Execution halted >> >> >> On my machine (MacOS with R 3.4.4) it works >> >> * creating vignettes ... OK >> >> Any suggestion of why this might happen? Is there something I am >> missing? >> >> Radu >> >> >> >> -- Hervé Pagès >> >> Program in Computational Biology >> Division of Public Health Sciences >> Fred Hutchinson Canc >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__maps. >> google.com_-3Fq-3DFred-2BHutchinson-2BCanc-26entry- >> 3Dgmail-26source-3Dg&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7 >> q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=sC2oO3c16mMorqdk5 >> d8nvHzqg1dL7v228YdPl836xng&s=9d0yj_ILpvoHB0vJLvElIr7feDGWvi >> gQCz4J4bsuCbo&e=>er >> Research Center >> 1100 Fairview Ave. N, M1-B514 >> P.O. Box 19024 >> Seattle, WA 98109-1024 >> >> E-mail: hpa...@fredhutch.org <mailto:hpa...@fredhutch.org> >> Phone: (206) 667-5791 >> Fax: (206) 667-1319 >> >> >> >> >> -- >> Best regards, >> >> Dr Nicolae Radu Zabet >> Lecturer in Computational Biology, >> School of Biological Sciences, University of Essex, >> Colchester, CO4 3SQ, United Kingdom >> T: +44(0)1206872630 >> E: nza...@essex.ac.uk <mailto:nza...@essex.ac.uk> >> > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpa...@fredhutch.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > -- Best regards, Dr Nicolae Radu Zabet Lecturer in Computational Biology, School of Biological Sciences, University of Essex, Colchester, CO4 3SQ, United Kingdom T: +44(0)1206872630 E: nza...@essex.ac.uk [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel